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Color-luminance interaction: data produced by oblique cross masking.

Threshold-elevation (TE-) versus-mask-spatial-frequency (SF) curves and TE-versus-mask-contrast curves, produced by the oblique-masking technique, were reported for uncrossed stimuli (color-test-on-color-mask and luminance-test-on-luminance-mask) [Invest. Ophthalmol. Visual Sci. Suppl. 34, 751 (1993) and Vision. Res. 23, 873 (1983)]. The technique minimizes the artifacts that are due to spatial phase effects, spatial beats, spatial probability summation, and local cues. My goal was to measure these curves for crossed stimuli (color-test-on-luminance-mask and luminance-test-on-color-mask) by this oblique-masking technique and to compare the curves with those reported in previous studies. For this purpose threshold contrasts were measured by a yes-no procedure with randomized double staircases. Test targets were vertical spatially localized (D6) patterns, and masks were oblique sinusoidal patterns; both the test and the mask were presented simultaneously, for 2 s (Gaussian window), on a color monitor interfaced with an ATVista system and a Powell achromatizing lens. The test SF's were 0.125, 0.5, 2, 4, and 8 cycles per degree (cpd); mask SF's were 0.031-16 cpd; and mask contrasts were 6.25%-50%. Furthermore, the Red-Green channel was defined by the minimum flicker and the hue cancellation techniques. Results show mostly masking effect (TE > 1) at contrasts above threshold; sometimes, separability (TE = 1) and above-threshold facilitation (TE < 1) effects were also observed, depending on the test SF, the mask SF, the mask contrast, and the subject. In general, the magnitudes of TE's are smaller and the TE-versus-mask-SF curves are slightly narrower for the oblique-cross-masking conditions than those for the respective oblique uncross masking. In addition, the TE-versus-mask-contrast curves for the crossed conditions are mostly shallower than those for the respective uncrossed conditions. Furthermore, mostly the color-luminance asymmetry (color masks luminance more than luminance masks color) is found, in mild form, for SF's > or = 0.5 cpd. For the lower SF of 0.125 cpd, there is either a lack of asymmetry or a very mild asymmetry of the opposite kind (luminance masks color slightly more than color masks luminance) seems to prevail. In general, the oblique-masking data shows mild asymmetry and reduced facilitation; both are consistent with reduced local cues, similar to those shown by randomized phase data, thus making the data suitable for SF analysis; moreover, at high contrast, the masking data are consistent with those reported in previous studies.

Adult↗

Evaluation of normalization methods for cDNA microarray data by k-NN classification.

BACKGROUND: Non-biological factors give rise to unwanted variations in cDNA microarray data. There are many normalization methods designed to remove such variations. However, to date there have been few published systematic evaluations of these techniques for removing variations arising from dye biases in the context of downstream, higher-order analytical tasks such as classification. RESULTS: Ten location normalization methods that adjust spatial- and/or intensity-dependent dye biases, and three scale methods that adjust scale differences were applied, individually and in combination, to five distinct, published, cancer biology-related cDNA microarray data sets. Leave-one-out cross-validation (LOOCV) classification error was employed as the quantitative end-point for assessing the effectiveness of a normalization method. In particular, a known classifier, k-nearest neighbor (k-NN), was estimated from data normalized using a given technique, and the LOOCV error rate of the ensuing model was computed. We found that k-NN classifiers are sensitive to dye biases in the data. Using NONRM and GMEDIAN as baseline methods, our results show that single-bias-removal techniques which remove either spatial-dependent dye bias (referred later as spatial effect) or intensity-dependent dye bias (referred later as intensity effect) moderately reduce LOOCV classification errors; whereas double-bias-removal techniques which remove both spatial- and intensity effect reduce LOOCV classification errors even further. Of the 41 different strategies examined, three two-step processes, IGLOESS-SLFILTERW7, ISTSPLINE-SLLOESS and IGLOESS-SLLOESS, all of which removed intensity effect globally and spatial effect locally, appear to reduce LOOCV classification errors most consistently and effectively across all data sets. We also found that the investigated scale normalization methods do not reduce LOOCV classification error. CONCLUSION: Using LOOCV error of k-NNs as the evaluation criterion, three double-bias-removal normalization strategies, IGLOESS-SLFILTERW7, ISTSPLINE-SLLOESS and IGLOESS-SLLOESS, outperform other strategies for removing spatial effect, intensity effect and scale differences from cDNA microarray data. The apparent sensitivity of k-NN LOOCV classification error to dye biases suggests that this criterion provides an informative measure for evaluating normalization methods. All the computational tools used in this study were implemented using the R language for statistical computing and graphics.

Algorithms↗

Spatial-tuning properties of auditory neurons in the optic tectum of the pigeon.

We studied the auditory neurons in the optic tectum of the unanesthetized pigeon, using single-unit recordings and acoustic free-field stimulation. Most units showed spatial tuning, with best areas located in the contralateral hemifield. All units responded also to visual stimuli, the auditory best areas being in rough alignment with visual receptive fields.

Acoustic Stimulation↗

The Speech, Spatial and Qualities of Hearing Scale (SSQ).

The Speech, Spatial and Qualities of Hearing Scale (SSQ) is designed to measure a range of hearing disabilities across several domains. Particular attention is given to hearing speech in a variety of competing contexts, and to the directional, distance and movement components of spatial hearing. In addition, the abilities both to segregate sounds and to attend to simultaneous speech streams are assessed, reflecting the reality of hearing in the everyday world. Qualities of hearing experience include ease of listening, and the naturalness, clarity and identifiability of different speakers, different musical pieces and instruments, and different everyday sounds. Application of the SSQ to 153 new clinic clients prior to hearing aid fitting showed that the greatest difficulty was experienced with simultaneous speech streams, ease of listening, listening in groups and in noise, and judging distance and movement. SSQ ratings were compared with an independent measure of handicap. After differences in hearing level were controlled for, it was found that identification, attention and effort problems, as well as spatial hearing problems, feature prominently in the disability handicap relationship,. along with certain features of speech hearing. The results implicate aspects of temporal and spatial dynamics of hearing disability in the experience of handicap. The SSQ shows promise as an instrument for evaluating interventions of various kinds, particularly (but not exclusively) those that implicate binaural function.

Aged↗

Optimal mapping of site-specific multivariate soil properties.

This paper demonstrates how geostatistics and fuzzy k-means classification can be used together to improve our practical understanding of crop yield-site response. Two aspects of soil are important for precision farming: (a) sensible classes for a given crop, and (b) their spatial variation. Local site classifications are more sensitive than general taxonomies and can be provided by the method of fuzzy k-means to transform a multivariate data set with i attributes measured at n sites into k overlapping classes; each site has a membership value mk for each class in the range 0-1. Soil variation is of interest when conditions vary over patches manageable by agricultural machinery. The spatial variation of each of the k classes can be analysed by computing the variograms of mk over the n sites. Memberships for each of the k classes can be mapped by ordinary kriging. Areas of class dominance and the transition zones between them can be identified by an inter-class confusion index; reducing the zones to boundaries gives crisp maps of dominant soil groups that can be used to guide precision farming equipment. Automation of the procedure is straightforward given sufficient data. Time variations in soil properties can be automatically incorporated in the computation of membership values. The procedures are illustrated with multi-year crop yield data collected from a 5 ha demonstration field at the Royal Agricultural College in Cirencester, UK.

Crops, Agricultural↗

Temporal and spatial integration in dynamic random-dot stimuli.

Random-dot cinematograms comprising many different, spatially intermingled local motion vectors can produce a percept of global coherent motion in a single direction. Thresholds for discriminating the direction of global motion were measured under various conditions. Discrimination thresholds increased with the width of the distribution of directions in the cinematogram. Thresholds decreased as the duration of area of the cinematogram increased. Temporal integration for global direction discrimination extends over about 465 msec (9.3 frames) while the spatial integration limit is at least as large as 63 deg2 (circular aperture diameter = 9 deg). The large spatial integration area is consistent with the physiology of higher visual areas such as MT and MST.

Discrimination, Psychological↗

Localization of harmonics generated in nonlinear shallow water waves.

The propagation of nonlinear shallow water waves over a random seabed is studied. A bathymetry which fluctuates randomly from a constant mean adds multiple scattering to resonant interactions and harmonic generation. By the method of multiple scales, nonlinear evolution equations for the harmonic amplitudes are derived. Effects of multiple scattering are shown to be represented by certain linear damping terms with complex coefficients related to the correlation function of the seabed disorder. For any finite number of harmonics, an equation governing the total wave energy is derived. By numerical solution of the amplitude equations, the effects of spatial attenuation (localization) on harmonic generation are studied.

Journal Article↗

MR angiography of the great anterior radiculomedullary artery (Adamkiewicz artery) validated by digital subtraction angiography.

BACKGROUND AND PURPOSE: Imaging of the anterior superficial spinal cord arteries by MR angiography is hindered by their small calibers and the similarity in configuration with the anterior superficial spinal cord veins. To validate the location and spatial configuration of the great anterior radiculomedullary artery, (ie, the Adamkiewicz artery [AKA]), contrast-enhanced MR angiography (CE-MRA) was compared with digital subtraction angiography (DSA). METHODS: Fifteen patients with suspected spinal cord vascular pathology underwent both spinal CE-MRA and selective spinal DSA. Two phase CE-MRA was performed with the use of a centric k-space filling scheme synchronized to the contrast bolus arrival. The level and side of the AKA origin were scored on the DSA and CE-MRA images and compared regarding image quality in terms of vessel conspicuity, contrast, continuity, sharpness, and background homogeneity on a relative 5-point scale. RESULTS: Localization and spatial configuration of the AKA by CE-MRA was in agreement with DSA findings in 14 of 15 cases. One mismatch of 1 vertebral level (not side) appeared as a result of the tangled vascular pathology. Comparison of image quality revealed that DSA is superior to CE-MRA concerning vessel continuity, sharpness, and background homogeneity (P < .001). Overall vessel conspicuity and contrast were judged to be similar. CONCLUSION: CE-MRA can visualize and localize the level of the AKA correctly. Image quality of CE-MRA is sufficient for detection of the AKA but is inferior to DSA.

Adult↗

Expression of the UDP-GalNAc: polypeptide N-acetylgalactosaminyltransferase family is spatially and temporally regulated during Drosophila development.

The UDP-GalNAc : polypeptide N-acetylgalactosaminyltransferase (ppGaNTase or ppGalNAcT or pgant) enzyme family is responsible for the first committed step in the synthesis of mucin-type O-glycans on protein substrates. Previous work from our group has demonstrated both sequence and functional conservation between members of this family in mammals and the fruit fly, Drosophila melanogaster. One member of this family in Drosophila has been shown to be essential for viability and development. In an effort to understand the developmental stages and processes in which O-glycosylation is involved, we have determined the expression pattern of each functional family member as well as putative isoforms during Drosophila development. Our studies indicate that isoforms are expressed in discrete spatial and temporal fashions during development, with some isoforms being found uniquely in restricted areas of the developing embryo (brain, trachea, pharynx, esophagus, proventriculus, and amnioserosa), whereas others are found in multiple regions and overlap with the expression of other isoforms (salivary glands, posterior midgut, anterior midgut, and the fore-/hindgut) during embryogenesis. Additionally, we examined expression patterns in imaginal discs from third instar larvae, which will become the adult structures. Most isoforms are also expressed in the imaginal discs, with some showing unique transcript localization and spatial regulatory control. Thus, this report provides insight into the specific regions during Drosophila development that may require O-linked glycosylation in vivo as well as which isoforms may act cooperatively in certain tissues and which may be uniquely responsible for glycosylation in others.

Animals↗

Native tesmin is a 60-kilodalton protein that undergoes dynamic changes in its localization during spermatogenesis in mice.

Tesmin is a testis-specific protein. Four mouse tesmin cDNAs so far reported encode a testis-specific, metallothionein-like, 30-kDa protein (tesmin-30). An antibody against tesmin-30, however, detected a protein of 60 kDa (tesmin-60) from the mouse testis. To resolve the relationship between the two, the immunoprecipitated native tesmin-60 was sequenced. The result indicated that tesmin-30 is not full-length but is part of the C-terminal half of tesmin-60. The full-length cDNA (2.2 kilobases [kb]) encoding tesmin-60 (475 amino acid residues) and its genomic DNA (23 kb) were cloned and sequenced. A search of databases indicated that tesmin is a member of the CXC-hinge-CXC family. Immunohistochemistry indicated that tesmin exhibits dynamic subcellular localization changes during spermatogenesis. Before meiosis, it was localized in the cytoplasm of early to late spermatocytes and then translocated into the nucleus just before meiotic division. After meiosis, it appeared in spermatids, starting from the acrosomal vesicles, moving to the nuclear membrane and then to the caudal end as the spermatids elongated, and finally relocating into the cytoplasm. Oxidative stress by cobalt chloride, as well as by diethylmaleate, induced both premature translocation of tesmin from the cytoplasm to the nucleus and apoptotic signals in spermatocytes. The persistent existence of tesmin and its temporally and spatially dynamic localization suggest that tesmin is involved in multiple stages of spermatogenesis and spermiogenesis, possibly during sperm maturation and/or morphogenesis.

Animals↗

Cell cycle-regulated nuclear localization of MCM2 and MCM3, which are required for the initiation of DNA synthesis at chromosomal replication origins in yeast.

MCM2 and MCM3 are two genetically interacting and structurally related proteins essential for growth in Saccharomyces cerevisiae. Mutants defective in these proteins affect the stability of minichromosomes in general, but the severity of the defect is dependent on the autonomously replicating sequence (ARS) that drives the replication of that plasmid. In this paper we show by two-dimensional gel electrophoresis that the initiation of DNA synthesis at chromosomal replication origins is also reduced in frequency in these mutants. We show further that the nuclear and subnuclear localizations of the MCM2 and MCM3 proteins are temporally regulated with respect to the cell cycle. These proteins enter the nucleus at the end of mitosis, persist there throughout G1 phase, and disappear from it at the beginning of S phase. Once inside the nucleus, a fraction of the MCM2 and MCM3 proteins becomes tightly associated with DNA. The association of MCM2 and MCM3 with chromatin presumably leads to the initiation of DNA synthesis, and their subsequent disappearance from the nucleus presumably prevents reinitiation of DNA synthesis at replication origins. This temporally and spatially restricted localization of MCM2 and MCM3 in the nucleus may serve to ensure that DNA replication occurs once and only once per cell cycle.

Cell Cycle↗

Opposite alterations of DNA methyltransferase gene expression in endometrioid and serous endometrial cancers.

OBJECTIVE: To examine the DNA methyltransferase (DNMT) mRNA and protein levels in endometrioid and serous cancers and to study the relationship between DNA methyltransferase expression and endometrial cancer development. METHODS: Normal endometrium, Grade I and Grade III endometrioid carcinoma tissues and cell lines, as well as serous cancer tissues, were analyzed for DNMT expression. Real-time PCR and Western blot techniques were employed to measure the mRNA and protein levels of the four DNA methyltransferases, DNMT1, DNMT2, DNMT3A, and DNMT3B. Immunohistochemistry was performed to detect alterations in DNMT nuclear localization and spatial organization patterns. RESULTS: While DNMT2 and DNMT3A expression appear to be normal, two- to fourfold increase in DNMT1 and DNMT3B were found in both Grade I and Grade III endometrioid cancers. In addition, the poorly differentiated cell lines expressed relatively higher DNMT levels than well-differentiated cells. In contrast to endometrioid carcinomas, serous cancers expressed substantially lower levels of DNMT1 and DNMT3B than normal controls, with four- and twofold reduction observed in DNMT1 and DNMT3B mRNA levels, respectively. Western blot analysis confirmed opposite expression patterns of DNMT1 and DNMT3B protein in endometrioid and serous cancers. Immunohistochemistry showed normal nuclear localization of DNMT1 and DNMT3B in Type I and Type II cancer specimens as well as cell cultures. CONCLUSION: Two opposite DNMT expression patterns were identified in endometrioid and serous cancers. The concerted upregulation in maintenance and de novo DNA methyltransferases in endometrioid carcinomas is consistent with a tendency for gene-specific hypermethylation observed in this histologic subtype, and may be implicated in tumor suppressor silencing. In contrast, the downregulation of maintenance and de novo DNA methyltransferases in serous cancers suggests that these tumors may contain hypomethylated genomic DNA, which has been associated with a higher mutation rate and is consistent with the known pathogenesis of serous-specific phenotypes. Taken together, the data suggest that divergent DNA methylation pathways may be implicated in the development of Type I and Type II endometrial cancers.

Carcinoma, Endometrioid↗

Spatial correlations of laminar BOLD and CBV responses to rat whisker stimulation with neuronal activity localized by Fos expression.

The spatial relationship between a measured fMRI signal and its underlying neuronal activity remains unclear. One obstacle is the localization of neuronal activity; another is the spatial resolution of fMRI. In the present study, high-resolution BOLD and CBV fMRI experiments (voxel size: 156 x 156 x 2000 microm3) were conducted in the rat whisker barrel cortex at 3 T; neuronal activity across cortical layers was mapped using the Fos expression technique. Results show that BOLD response is weighted by blood volume and that pixels with high BOLD response can be located at the cortical surface or in deep layers, depending on local vasculature. In contrast to BOLD response, the pixels with high CBV response were consistently clustered in the deep cortical layers. Percentage-CBV change in cortical layers IV-V was 7.3 +/- 1.5%, which was significantly higher than in layers I-III (4.1 +/- 0.9%) and VI (4.3 +/- 0.7%) (mean +/- SEM). The laminar distribution of CBV response correlates well with neuronal activity localized by Fos expression. We conclude that neuronal activity can be inferred from CBV fMRI data with high spatial accuracy. The data indicate that both intracolumn functional connectivity and neurovascular coupling can be studied using CBV fMRI.

Animals↗

Processing radio frequency ultrasound images: a robust method for local spectral features estimation by a spatially constrained parametric approach.

Spectral estimation is a major component in studies aiming at characterizing biological tissues through the analysis of backscattered radio frequency (RF) ultrasonic signals and images. However, conventional spectral estimation techniques yield a well-known trade-off between spatial resolution and variance. The backscattered signals are stochastic by nature, so short-term local analysis results in a high variance of the estimates, which cannot efficiently be reduced through conventional spatial averaging. We address this issue by describing a spectral estimation technique that reduces the variance of the estimates (by smoothing the local estimates in spectrally homogeneous regions) while preserving spectral discontinuities (i.e., the smoothing is not performed across regions with different spectral contents). The proposed approach is set in a Bayesian framework and is based on local autoregressive (AR) estimation, constrained by smoothness priors. These smoothness priors are introduced through a Markov random field in which the associated potential functions are nonquadratic, allowing thereby to preserve discontinuity. The method is validated on simulated RF images and tested on echocardiographic images acquired in vivo. The results are compared to the estimates provided by the conventional Burg technique. These results clearly demonstrate the ability of the proposed approach to improve spectral estimation in terms of variance reduction and discontinuity detection.

Algorithms↗

Audio and visual cues in a two-talker divided attention speech-monitoring task.

Although audiovisual (AV) cues are known to improve speech intelligibility in difficult listening environments, little is known about their role in divided attention tasks that require listeners to monitor multiple talkers at the same time. In this experiment, a call-sign-based multitalker listening test was used to evaluate performance in two-talker AV configurations that combined zero, one, or two channels of visual information (neither, one, or both talkers visible) with zero, one, or two channels of audio information (no audio, both talkers played from the same loudspeaker, and both talkers played through different, spatially separated loudspeakers). The results were analyzed to determine the relative performance levels that would occur with each AV configuration with target information that was equally likely to originate from either of the two talkers in the stimulus. The results indicate that spatial separation of the audio signals has the greatest impact on performance in multichannel AV speech displays and that caution should be used when presenting a visual representation of only a single talker unless that talker is known to be the highest priority talker in the combined AV stimulus. Potential applications of this research include the design of improved audiovisual speech displays for multichannel communications systems.

Adult↗

Enhancement of neuroplastic P2 and N1c auditory evoked potentials in musicians.

P2 and N1c components of the auditory evoked potential (AEP) have been shown to be sensitive to remodeling of the auditory cortex by training at pitch discrimination in nonmusician subjects. Here, we investigated whether these neuroplastic components of the AEP are enhanced in musicians in accordance with their musical training histories. Highly skilled violinists and pianists and nonmusician controls listened under conditions of passive attention to violin tones, piano tones, and pure tones matched in fundamental frequency to the musical tones. Compared with nonmusician controls, both musician groups evidenced larger N1c (latency, 138 msec) and P2 (latency, 185 msec) responses to the three types of tonal stimuli. As in training studies with nonmusicians, N1c enhancement was expressed preferentially in the right hemisphere, where auditory neurons may be specialized for processing of spectral pitch. Equivalent current dipoles fitted to the N1c and P2 field patterns localized to spatially differentiable regions of the secondary auditory cortex, in agreement with previous findings. These results suggest that the tuning properties of neurons are modified in distributed regions of the auditory cortex in accordance with the acoustic training history (musical- or laboratory-based) of the subject. Enhanced P2 and N1c responses in musicians need not be considered genetic or prenatal markers for musical skill.

Acoustic Stimulation↗

Multimodal Analysis Reveals Aberrant Expression of SUMO2 and Its Significant Association With Key Mechanisms of Metabolic Pathways in Hepatocellular Carcinoma.

BACKGROUND: Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related deaths worldwide. However, the role of small ubiquitin-like modifier 2 (SUMO2), a core member of the small ubiquitin-like modifier (SUMO) family, regarding its expression patterns and metabolism-related functions in HCC remains inadequately understood. METHODS: A multidimensional analytical framework was applied, integrating immunohistochemistry (153 HCC vs. 21 non-HCC samples), proteomics (159 paired samples), bulk transcriptomics (3240 HCC vs. 2267 non-HCC samples), single-cell RNA sequencing (RNA-seq) (10 HCC vs. 8 non-HCC samples), spatial transcriptomics, and external CRISPR/Cas9 functional genomics data. Systematic analyses included standardized mean difference (SMD), pathway enrichment, pseudotime trajectory inference, in silico knockout, cell-cell communication, metabolic flux scoring, immune infiltration, clinical correlation, drug sensitivity prediction, and molecular docking. RESULTS: At the protein level, immunohistochemistry (nuclear positivity) and external proteomic data collectively demonstrated consistent SUMO2 overexpression in HCC. Consistent upregulation was also observed at the mRNA level across large-scale cohorts. Single-cell RNA-seq and spatial transcriptomics localized SUMO2 enrichment to malignant hepatocytes and tumor-dominant regions. CRISPR-mediated SUMO2 knockout suppressed proliferation in multiple HCC cell lines. Mechanistically, high SUMO2 expression was significantly associated with metabolic reprogramming involving glycolysis/gluconeogenesis, pyruvate metabolism, and the tricarboxylic acid cycle. SUMO2-high malignant hepatocyte subpopulations exhibited enhanced activity of the macrophage migration inhibitory factor signaling axis and enhanced iron-sensor interactions. Further, the immune infiltration analysis revealed a negative correlation between SUMO2 expression and M1 macrophages and a positive correlation between follicular helper T cells and regulatory T cells. Clinically, elevated SUMO2 levels were found to be associated with adverse prognostic features. Furthermore, high SUMO2 expression was associated with increased sensitivity to dasatinib, and molecular docking simulations predicted potential binding between SUMO2 and dasatinib, with a Vina score of -8.5 kcal/mol. CONCLUSIONS: SUMO2 is aberrantly expressed at the protein, mRNA, single-cell, and spatial transcriptomic levels in HCC and is significantly associated with metabolic reprogramming and altered migration inhibitory factor (MIF)-mediated intercellular communication, suggesting its potential as a novel biomarker for diagnosis and treatment.

Humans↗

Localization of a peripheral patch: the role of blur and spatial frequency.

Peripheral vision serves to direct our attention and fixation to objects of interest. This requires that the visual system be capable of accurately localizing peripherally presented targets having different spatial structures. The question we address is "to what extent does stimulus spatial structure influence the precision of peripheral localization?" To address this issue, we measured the precision of spatial localization (with reference to a foveal target) for a single Gaussian or Gabor patch briefly presented in the periphery. For both stimuli, we find that when the standard deviation of the stimulus envelope (SD) is less than 1/5 the stimulus eccentricity, localization thresholds are independent of SD and are approximately 1/50 of eccentricity. For larger values of SD, localization thresholds increase linearly with increasing SD, and are approximately 1/5 of SD. The results hold over a range of eccentricities (from 2.5 to 10 deg) and stimulus contrasts (from near detection threshold to 80%). In addition, for Gabor patches, the results are independent of frequency, phase and orientation of the carrier.

Humans↗